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Abstract
The single species Brassica oleracea has great economic importance, remarkable morphological variation and unusual genome complexity. Nuclear DNA variations suggest that the Brassica oleracea morphotypes can be divided into three groups, with Chinese kale as one, cauliflower and broccoli as another and the other morphotypes as the third. In this study, we aim to investigate the genetic control of morphological variation through two approaches. First, to dissect the genetics of morphological diversity within the species, three accessions, one from each of three major clades in B. oleracea, were used to construct two backcross populations. Inbred lines of cabbage [B. oleracea var. capitata L., ‘Badger Inbred’ (BIL)] and cauliflower [B. oleracea var. botrytis L., mutant for Orange gene (ORG)] were used as donor parents, and a rapid cycling line (TO1434) as common recurrent parent. From the populations, we have selected 96 and 104 introgression lines representing 81.15% and 78.56% of the cabbage and cauliflower genomes, respectively. A total of 109 and 141 marker-trait associations were found for 15 leaf-, stem-, and flower-traits across eight seasons in the cabbage and cauliflower population, respectively. Major QTL can be dissected to as fine as 0.9 MB, which illustrates the value of the developed populations. Comparative analyses of QTLs between the two populations suggest that cabbage and cauliflower do not share same genetic basis in morphological variation. However, sequence analyses and common marker-trait associations indicate that there might be common genetic features between cabbage and cauliflower. Second, we investigate the genome-wide distribution of nonreciprocal DNA exchanges between paralogs and its relationship to morphological variation within the species. We discover 266,512 polymorphic paralogous sites with single nucleotide variation among 25 B. oleracea accessions. In summary, 97,544 and 55,104 sites show conversion and mutation, respectively. Distributions of conversions have suggested that the conversion process is highly related to homologous gene number. The gene ontologies of Arabidopsis thaliana orthologs of converted genes are enriched in terms related to morphology, which might suggest a relationship between conversion and morphological variation. Genes with conversion signals residing in regions under selective constraint might be potential candidate genes contributing to morphological variation.